This sounds very much off topic and freebsd specific. But /usr/src/sys is the kernel source, /usr/src/usr.bin is the source for the userland applications in /usr/bin. The userland sources need to be installed explicitly (are not installed by default) to modify userland tools.
http://www.freebsd.org/doc/en/books/handbook/makeworld.htmlBut I would suggest looking for existing native authentication such as
net/nss_ldap and
security/pam_ldap which allow use of ldap for storage. The nss_ldap at might provide nss capability usable the standard userland commands with an ldap backend.
Cheers
Brett